背景:趋磁细菌(MTB)是一组独特的微生物,它们通过生物矿化磁性纳米颗粒来感知和导航通过地磁场。来自Nitrospirota门(以前称为Nitrospirae)的MTB在各种水生生态系统中茁壮成长。由于每个细胞产生数百个磁铁矿(Fe3O4)磁小体纳米颗粒,因此它们引起了极大的兴趣,远远超过其他MTB。形态学,系统发育,并且已经对NitrosirotaMTB的基因组多样性进行了广泛的研究。然而,由于缺乏栽培技术,硝基螺旋体MTB的代谢和生态生理学在很大程度上是未知的。
方法:这里,我们建立了一种联系形态学的方法,基因组,使用纳米级二次离子质谱(NanoSIMS)结合基于rRNA的原位杂交和靶标特异性微型宏基因组学,在单细胞水平上对未培养的NitrosirotaMTB群体(命名为LHC-1)进行代谢研究。
结果:我们从淡水湖中磁性分离了LHC-1,并使用基因组解析的微型宏基因组学重建了LHC-1的基因组草案。我们发现10个LHC-1细胞足以作为模板获得高质量的基因组草图。基因组分析显示,LHC-1具有固定CO2和还原NO3的潜力,随着时间的推移,通过结合稳定同位素孵育和NanoSIMS分析,在单细胞水平进一步表征。此外,NanoSIMS结果揭示了LHC-1中特定的元素分布,并且不同LHC-1细胞之间CO2和NO3-代谢的异质性随孵育时间增加。
结论:据我们所知,这项研究提供了个体NitrosirotaMTB细胞的首次代谢测量,以破译其生态生理特征。本研究中构建的程序提供了一个有希望的策略来同时研究形态学,基因组,和自然环境中未培养微生物的生态生理学。视频摘要。
BACKGROUND: Magnetotactic bacteria (MTB) are a unique group of microorganisms that sense and navigate through the geomagnetic field by biomineralizing magnetic nanoparticles. MTB from the phylum Nitrospirota (previously known as Nitrospirae) thrive in diverse aquatic ecosystems. They are of great interest due to their production of hundreds of magnetite (Fe3O4) magnetosome nanoparticles per cell, which far exceeds that of other MTB. The morphological, phylogenetic, and genomic diversity of Nitrospirota MTB have been extensively studied. However, the metabolism and
ecophysiology of Nitrospirota MTB are largely unknown due to the lack of cultivation techniques.
METHODS: Here, we established a method to link the morphological, genomic, and metabolic investigations of an uncultured Nitrospirota MTB population (named LHC-1) at the single-cell level using nanoscale secondary-ion mass spectrometry (NanoSIMS) in combination with rRNA-based in situ hybridization and target-specific mini-metagenomics.
RESULTS: We magnetically separated LHC-1 from a freshwater lake and reconstructed the draft genome of LHC-1 using genome-resolved mini-metagenomics. We found that 10 LHC-1 cells were sufficient as a template to obtain a high-quality draft genome. Genomic analysis revealed that LHC-1 has the potential for CO2 fixation and NO3- reduction, which was further characterized at the single-cell level by combining stable-isotope incubations and NanoSIMS analyses over time. Additionally, the NanoSIMS results revealed specific element distributions in LHC-1, and that the heterogeneity of CO2 and NO3- metabolisms among different LHC-1 cells increased with incubation time.
CONCLUSIONS: To our knowledge, this study provides the first metabolic measurements of individual Nitrospirota MTB cells to decipher their ecophysiological traits. The procedure constructed in this study provides a promising strategy to simultaneously investigate the morphology, genome, and
ecophysiology of uncultured microbes in natural environments. Video Abstract.